marcc-hpc/gatk:latest

$ singularity pull shub://marcc-hpc/gatk:latest

Singularity Recipe

Bootstrap: docker
From: broadinstitute/gatk
IncludeCmd: yes

%environment
  # use bash as default shell
  SHELL=/bin/bash
  export SHELL

%setup
  # runs on host - the path to the image is $SINGULARITY_ROOTFS

%post
  # post-setup script

  # load environment variables
  . /environment

  # use bash as default shell
  echo 'SHELL=/bin/bash' >> /environment

  # make environment file executable
  chmod +x /environment

  # default mount paths
  mkdir -p /scratch /data 

%test
  # test that script is a success

Collection

• Name: marcc-hpc/gatk
• License: MIT License

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